Author

J. I. Sulkowska

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 4

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 4 Approach:experimental assay· 3 Assay:protein structure· 3 Approach:statistical model· 3 Organism:human· 2 Organism:bacteria (other)· 1 Approach:deep learning· 1 Approach:mechanistic / dynamical model· 1

Frequent Co-Authors

A. P. Perlinska· 2 shared I. Lewandowska· 2 shared R. Augustyniak· 2 shared S. Niewieczerzal· 2 shared A. Kluza· 1 shared A. Stasiulewicz· 1 shared B. Belza· 1 shared E. Flapan· 1 shared

Activity by Year

2020-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBiophysics

A. P. Perlinska

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Proteins containing 6-crossing knot types andtheir folding pathways

M. Sikora, E. Flapan, H. Wong, P. Rubach, W. Garstka, S. Niewieczerzal, E. J. Rawdon, J. I. Sulkowska

This paper analyzes 6-crossing protein knots using AlphaFold 2 predictions and a coarse-grained model, identifying two distinct folding mechanisms for the 63 knot.

bioRxiv · Jun 16, 2023 · PreprintBiophysics

Nucleolar Essential Protein 1 (Nep1): Elucidation of Enzymatic Catalysis Mechanism by Combined Molecular Dynamics Simulation and Quantum Chemical Calculations

M. Jedrzejewski, B. Belza, I. Lewandowska, M. Sadlej, A. P. Perlinska, R. Augustyniak, T. Christian, Y.-M. Hou, M. Kalek, J. I. Sulkowska

This study elucidates the catalytic mechanism of Nep1 using molecular dynamics and quantum chemical calculations, revealing that water mediates proton transfer rather than a conserved serine residue.

bioRxiv · Mar 21, 2023 · PreprintBiophysics

First crystal structure of double knotted protein TrmD-Tm1570 - inside from degradation perspective

F. Bruno da Silva, I. Lewandowska, A. Kluza, S. Niewieczerzal, R. Augustyniak, J. I. Sulkowska

The paper presents the first crystal structure of a double knotted protein TrmD-Tm1570 and shows it can be degraded by the ClpXP system, with simulations explaining degradation kinetics.

bioRxiv · Mar 13, 2023 · PreprintBiophysics

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

A. P. Perlinska, A. Stasiulewicz, E. K. Nawrocka, K. Kazimierczuk, P. Setny, J. I. Sulkowska

The paper analyzes SAM conformational space in free and bound states, identifying structural differences between knotted and unknotted methyltransferases.

PLOS Computational Biology · May 26, 2020Peer-reviewedBiophysics